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Use pmcx instead of mcx binary #256

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lkeegan
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@lkeegan lkeegan commented Oct 4, 2023

Please check the following before creating the pull request (PR):

  • Did you run automatic tests?
  • Did you run manual tests?
  • Is the code provided in the PR still backwards compatible to previous SIMPA versions?

List any specific code review questions

List any special testing requirements

Additional context (e.g. papers, documentation, blog posts, ...)

Provide issue / feature request fixed by this PR

Fixes #

- input volume numpy array is passed directly to pmcx
  - avoids the need to write a binary mcx input file to disk
- output data directly provided by pmcx as numpy arrays
  - avoids the need to read mcx binary output files
- 5% reduction in optical model run-time for a test script
@kdreher
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kdreher commented Jun 25, 2024

We agreed on not using pmcx because of license issues.

@kdreher kdreher closed this Jun 25, 2024
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